New phylum of bacteria found lurking in hospital sink’s drain

Its genome hints that it may live inside some other organism.

Most of the life on Earth comes in the form of small, single-celled organisms. But even though we knew there was incredible diversity at the microbial level, these cells all look pretty similar under a microscope. For many of the bacterial species we've identified, the key step has been growing them in a flask so we can generate large enough numbers to study them.

Over the past decade, the advent of cheap DNA sequencing technology has helped the microbe discovery process along. Currently, we can sequence huge populations of microbes and get fragments of sequences that give us some sense of the full diversity of life. But these sequences tell us little more than the fact that a species exists. We still often know little about what it is and how it manages to make a living.

Now some researchers have managed to generate a genome sequence from a single bacterium, and they have used this technique to scan for new species in a biofilm isolated from a hospital sink. The results include the genome of a previously unrecognized phylum of bacteria, called TM6, that appears to be an obligate symbiote, perhaps living inside another cell found in the biofilm.

Researchers tend to work with bacteria that grow in a liquid culture but most bacteria don't live that way. Instead they form biofilms, a dense mesh of material that is inhabited by entire communities of bacteria and which hosts multiple species. It's easy to do some DNA sequencing to figure out how many species inhabit these biofilms, but finding out more about the species is tough, because many of them won't survive in the oxygen rich culture conditions that are typically used.

To get around this, an international team of researchers has developed a technique for isolating individual bacterial cells with a cell-sorting machine. At first, they kept isolating fragments of the biofilm rather than cells, so they ended up having to pool anywhere from 20-100 items the machine called "cells" in order to increase the chances of having a single cell present. Most of these cells were things we already knew about, so the authors started doing some quick checks of some key genes that encode ribosomal RNA. If those indicated the sample had a single cell and the cell wasn't already known, they produced an entire genome from it.

This week, the group released a paper on a genome from a group of species called TM6. The name comes from “Torf, Mittlere Schicht,” which is “peat, middle layer” in German. That's the first case instance where the ribosomal RNA for this group of species had appeared but since then it's been found in a host of environmental samples: domestic water sources, acidic cave biofilms, acid mine drainage biofilms, wastewater biofilms, soil, contaminated groundwater and subsurface sites, aquatic moss, hypersaline mats, peat bogs, and peat swamps. The ribosomal RNA had suggested it was distantly related to all the bacterial groupings we knew about, and now the genome confirms it.

Perhaps the most striking thing about it is the fact that fully 43 percent of the genes appear to encode proteins that we've never seen before. Typically, due to a combination of common descent and gene transfer, many of the genes in new species are familiar. This one is so far out, most of them don't look like anything we know about. Which, of course, makes it hard to predict what they might do.

In contrast, when it comes to familiar genes, many are missing in action. The TM6 genome seems to have a stripped down metabolism that's probably anaerobic. It doesn't seem to be able to make its own amino acids or nucleotides (protein and DNA components, respectively) and it can't make a flagella to move itself around. All of which suggests it's probably a symbiotic organism, cooperating with another species to share vital biochemicals that only one of the two can produce.

What might it be living with? Some of the genome hints that it may be a eukaryote like an amoeba. A few of the genes seem to contain sequences that are typically only found in eukaryotes (larger cells with a nucleus), suggesting they got in this new species via horizontal transfer of some DNA. This is quite common among bacteria that live inside their hosts, suggesting that TM6's host is a eukaryote. In the past, amoeba have been found in biofilms, which often carry a number of bacterial species along with them.

Overall, the genome sequences don't match up well with anything we know, suggesting that TM6 represents an entirely new phylum of bacteria. Its closest relatives are the Acidobacteria, which themselves had gone unrecognized until the 1990s. If this holds up, it will continue the bacteria's remarkable expansion. They started with just 11 phyla back in 1987, and most recent estimates now say that there are 30 bacterial phyla on the planet. TM6 is likely to make that count 31.

Who knows what we'll find when we start looking beyond a hospital sink's drain.

My first thought was that, given their 1-2 billion year head start on multicellular life, bacteria might be so deeply separated as a kingdom that phyla might be more analogous to orders or genera in animals: not true. Here I see only 23-29 here (http://en.wikipedia.org/wiki/Bacteria). I wonder, though, if we won't eventually reach such a position, given the age difference I mention above and how little we currently know about bacteria.

Oxygen readily penetrates biofilm. While the bacteria in question may be anaerobic it does not follow that oxygen will kill it. Such bacteria are usually referred to as "facultative". There are many reasons why a bacteria may not be easy to culture. Such bacteria are referred to as "fastidious". Often the obstacle is figuring out which nutrients are needed.

n,b,: about 400 different bacterial species are found in the mouth, many of which have never been cultured.

A hospital near where I live considered putting automatic soap pumps in their buildings to reduce bacteria. However, they soon found that the pumps themselves harbored far more dangerous bacteria. A bit of a scary fact since hospitals contain patients which have deficiencies in their immune system.

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Humans (and many other animals) don't make all of their own amino acids either.

My first thought was that, given their 1-2 billion year head start on multicellular life, bacteria might be so deeply separated as a kingdom that phyla might be more analogous to orders or genera in animals: not true. Here I see only 23-29 here (http://en.wikipedia.org/wiki/Bacteria). I wonder, though, if we won't eventually reach such a position, given the age difference I mention above and how little we currently know about bacteria.

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Viruses have no physiology of their own, and are basically just a packet of genetic information that moves between cells, and depends on cellular machinery to reproduce.

Bacteria like these maintain their membrane-bound state, maintain their own genome, maintain their own proteins, and maintain their own physiology. They are an endosymbiote or parasite, but they are still considered cellular life because they are still cells.

I enjoy reading this stuff. It serves as a solid reminder that - despite modern-day attitudes on knowledge and science - there really is so much out there we don't understand or aren't even aware of. I suppose that I understood that there were categories of bacteria that were anaerobic, but the idea that most might be that way and only a small fraction can even be bred in petri dishes - I didn't even know that I didn't know.

I enjoy reading this stuff. It serves as a solid reminder that - despite modern-day attitudes on knowledge and science - there really is so much out there we don't understand or aren't even aware of. I suppose that I understood that there were categories of bacteria that were anaerobic, but the idea that most might be that way and only a small fraction can even be bred in petri dishes - I didn't even know that I didn't know.

Keep it up, Ars!

Yeah, It seems the more we know the more we know we don't know. Its as if 96% of the universe was pretty much hidden from us.

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Viruses have no physiology of their own, and are basically just a packet of genetic information that moves between cells, and depends on cellular machinery to reproduce.

Bacteria like these maintain their membrane-bound state, maintain their own genome, maintain their own proteins, and maintain their own physiology. They are an endosymbiote or parasite, but they are still considered cellular life because they are still cells.

Not all viruses are snippets of RNA.

I was going off an old recollection that the most sophisticated viruses were basically cells except missing some essential machinery for reproduction, though I readily admit biology is not my field, and these new bacteria might qualify as fully alive.

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Humans (and many other animals) don't make all of their own amino acids either.

The article makes it sound like these critters can't make any of their amino acids.

Quote:

It doesn't seem to be able to make its own amino acids or nucleotides (protein and DNA components, respectively)

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Humans (and many other animals) don't make all of their own amino acids either.

The article makes it sound like these critters can't make any of their amino acids.

Quote:

It doesn't seem to be able to make its own amino acids or nucleotides (protein and DNA components, respectively)

The question of is it a virus,..... bacteria, .....alive is fraught with conundrums. Probably a spectrum along the way.

I know there's a concern. Just how far down the drain is what I want to know. Are these bacteria found 10 feet from the surface of the sink or merely few inches below the sink? It makes a big difference right there. There must be a whole bunch more bacteria found a couple of miles down the drain pipes leading to the ocean should also a health risk. No?

Another thing is, is this research paper subjecting us that the household all purpose cleaners we daily using to clean our sinks won't kill any of these bacteria? That doesn't sounds any true. Because I know it won't be that case. Then why we even bother to spend our money for these cleaning solutions?

The jpeg presented on this research may be just a demonstration for this article to describe the health risk situation in a hospital environment. In real life, if the hospital is belongs to city property, the hospital should be under a scheduled inspection of a city health inspector to inspect the hospital periodically. If there are issues found in the sink such as this jpeg presented, (it looks nasty even in a picture), this city health inspector is liable for not doing his job and he should be fired right at the spot.

So my question would be, how realistic is this research telling us? We are not talking about some hospitals of third world or under developed country are we?

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Viruses have no physiology of their own, and are basically just a packet of genetic information that moves between cells, and depends on cellular machinery to reproduce.

Bacteria like these maintain their membrane-bound state, maintain their own genome, maintain their own proteins, and maintain their own physiology. They are an endosymbiote or parasite, but they are still considered cellular life because they are still cells.

Not all viruses are snippets of RNA.

I was going off an old recollection that the most sophisticated viruses were basically cells except missing some essential machinery for reproduction, though I readily admit biology is not my field, and these new bacteria might qualify as fully alive.

I don't intend to say that all viruses are just genetic material and nothing else. There are viruses that have envelopes, and more complex viruses that have larger genomes, like the Megavirus family. But all viruses shed these extra features and replicate inside the host cell right in the midst of our own proteins and machinery. They do not maintain a physical barrier between itself and the host cell, as bacteria like mycoplasma or listeria do.

Is anyone else super excited to find out what this thing does / makes in the cells it inhabits? Also if those new genes encode functioning proteins, what do they do? Exciting discovery, with a lot of follow-up potential.

Hospital sinks may contain a rich unexplored biotope, but I would rather collect my samples on a yacht, like Craig Venter's crue does.

We have only explored a tiny fraction of life on Earth, and we understand only a tiny fraction of the life that we've observed. Knowledge in this field holds the keys to a clean environment, health, renewable energy, and history of life on our planet.

Another fascinating detective story is Jane Koehler's discovery of the causative agent of "cat scratch fever," which can look like cancer in immunocompromised patients. It was another bacterium that multiplies only inside cat (or human) cells.She discovered the first species of Bartonella, and other species have since been discovered in other animals, one of which has been implicated in "trench fever," which afflicted many troops in World War I to the point that it affected military outcomes. Jane Koehler is at UCSF.

Awesome! I hope it turns out to be far more common then anyone realized, perhaps living in symbiosis with higher-level mult-cell organisms like us ala mitochondria. Then we can look forward to a whole new generation of Japanese bio-horror stories, video games and movies! :-p

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Viruses have no physiology of their own, and are basically just a packet of genetic information that moves between cells, and depends on cellular machinery to reproduce.

Bacteria like these maintain their membrane-bound state, maintain their own genome, maintain their own proteins, and maintain their own physiology. They are an endosymbiote or parasite, but they are still considered cellular life because they are still cells.

Not all viruses are snippets of RNA.

I was going off an old recollection that the most sophisticated viruses were basically cells except missing some essential machinery for reproduction, though I readily admit biology is not my field, and these new bacteria might qualify as fully alive.

I don't intend to say that all viruses are just genetic material and nothing else. There are viruses that have envelopes, and more complex viruses that have larger genomes, like the Megavirus family. But all viruses shed these extra features and replicate inside the host cell right in the midst of our own proteins and machinery. They do not maintain a physical barrier between itself and the host cell, as bacteria like mycoplasma or listeria do.

So the sophisticated viruses only inject the genetic material? Thanks, that makes the distinction between virus and simple cell much clearer. The teacher skipped that part, though it was a class for high school kids and thus highly simplified.

If it is likely reliant on symbiotic relationships and needs a host then they should stick it in a few different types of cells culture them and see what happens... :-D This would at least give them a chance to study it and see what some of the proteins it produces are.

Have you seen the latest biofilm? I think it's pretty hot.It's got some cool new characters (though it lacks a bit in plot).The lead's a chap who always knew he'd make it in the flix,Despite his parents calling him the catchy 'TM6'.Now some debate regarding whether he's properly alive;You'd have to check his brothers first; that's TM's one through five.Apparently George Lucas thinks his screen name should be Darth,Because he's from the dark side - the dark side of your bath...From waste pipes and obscurity to a quarter-hour of fameA bit part in evolution is a lead role in a drain.

i love stories like this, i find the human ego needs a regular bitch slapping to knock it down a bit from its own sense of superiority and "know-it-allness"

we may think we're all that and a bag of chips because we no longer live in caves, but in reality, all we've really accomplished can probably be equated to merely taking a single step out of a cave and looking around at all the bright and shiny things around us. In term of our understanding of the way the universe works is concerned at least.

If the organism can't make its own amino acids or nucleotides, doesn't that make it a virus? It's one thing to require an environment only found inside a host, but to be reliant for basic life processes seems to be that "semi-living" state reserved for the virus.

Of course, it's been a long time since I took biology class... maybe the classifications have been redone?

Viruses have no physiology of their own, and are basically just a packet of genetic information that moves between cells, and depends on cellular machinery to reproduce.

Bacteria like these maintain their membrane-bound state, maintain their own genome, maintain their own proteins, and maintain their own physiology. They are an endosymbiote or parasite, but they are still considered cellular life because they are still cells.

Not all viruses are snippets of RNA.

I was going off an old recollection that the most sophisticated viruses were basically cells except missing some essential machinery for reproduction, though I readily admit biology is not my field, and these new bacteria might qualify as fully alive.

I don't intend to say that all viruses are just genetic material and nothing else. There are viruses that have envelopes, and more complex viruses that have larger genomes, like the Megavirus family. But all viruses shed these extra features and replicate inside the host cell right in the midst of our own proteins and machinery. They do not maintain a physical barrier between itself and the host cell, as bacteria like mycoplasma or listeria do.

So the sophisticated viruses only inject the genetic material? Thanks, that makes the distinction between virus and simple cell much clearer. The teacher skipped that part, though it was a class for high school kids and thus highly simplified.

After the viral genome enters the cell, it (either DNA or RNA) encodes proteins that are produced in the host cell. These proteins can have a variety of functions, including polymerases for copying the viral genome, proteins for encapsidating the viral genome, and other proteins that can alter the host cell's functions. For example, a number of viruses make proteins that disable the cell's innate antiviral responses.